NGS

NGS, or Next-Generation Sequencing, is a high-throughput, massively parallel sequencing technology that enables rapid and cost-effective sequencing of DNA or RNA. It has revolutionized genomics research and clinical diagnostics by allowing the sequencing of entire genomes, exomes, or targeted regions of interest in a single experiment. Here’s how NGS testing works and its applications:

How NGS Works:

  1. Library Preparation: DNA or RNA samples are fragmented and adapters are ligated to the ends of the fragments. These adapters contain sequences necessary for amplification and sequencing.

  2. Amplification: The DNA fragments with adapters are then amplified through a process called polymerase chain reaction (PCR) to generate clusters of identical DNA fragments.

  3. Sequencing: The amplified DNA fragments are sequenced simultaneously in a massively parallel manner. Different NGS platforms use different sequencing chemistries, but the basic principle involves determining the sequence of each fragment in the sample.

  4. Data Analysis: The sequence data generated by NGS is processed using bioinformatics tools to align the sequence reads to a reference genome or transcriptome, identify genetic variants (e.g., single nucleotide polymorphisms, insertions, deletions), and interpret the functional consequences of these variants.

Applications of NGS Testing:

  1. Whole Genome Sequencing (WGS): WGS involves sequencing the entire genome of an organism. It can provide comprehensive information about an individual’s genetic makeup and is used in research settings to study genetic variation, population genetics, and disease risk.

  2. Whole Exome Sequencing (WES): WES focuses on sequencing the protein-coding regions of the genome, known as exons. It is used to identify genetic variants that are likely to have functional consequences and are associated with Mendelian disorders, cancer, and other diseases.

  3. Targeted Sequencing: Targeted sequencing involves sequencing specific regions of interest in the genome, such as genes associated with a particular disease or pathway. It is used in clinical diagnostics to identify known disease-causing mutations and assess pharmacogenomic variants relevant to drug response.

  4. RNA Sequencing (RNA-Seq): RNA-Seq involves sequencing the transcriptome, which comprises all the RNA molecules in a cell. It is used to quantify gene expression levels, identify alternative splicing events, and detect fusion genes or novel transcripts in diseases such as cancer.

  5. Metagenomic Sequencing: Metagenomic sequencing involves sequencing DNA from microbial communities in environmental samples or clinical specimens. It is used to characterize microbial diversity, identify pathogens, and study the microbiome’s role in health and disease.

NGS testing has numerous applications in research, clinical diagnostics, and personalized medicine. It has enabled advancements in genomics, oncology, infectious disease, and other fields by providing comprehensive and high-resolution genetic information.

NGS Most Popular Questions

Why use the Illumina TrueSight One Panel for NGS?

The Illumina TrueSight One Panel is a targeted next-generation sequencing (NGS) panel designed for clinical genetic testing applications. It offers several advantages and features that make it a valuable tool for genetic analysis in clinical settings:

Overall, the Illumina TrueSight One Panel offers a robust and reliable solution for clinical genetic testing, providing clinicians and patients with valuable genetic information for diagnosis, prognosis, and personalized treatment decisions in a wide range of genetic disorders.

Why is the Illumina TrueSight One Panel special?

The Illumina TrueSight One Panel stands out for several reasons, making it a special and valuable tool for genetic analysis in clinical settings:

  1. Comprehensive Coverage: The TrueSight One Panel offers comprehensive coverage of clinically relevant genes associated with a wide range of inherited diseases, including Mendelian disorders, cardiovascular conditions, neurological disorders, and cancer predisposition syndromes. Its extensive gene content allows for comprehensive genetic analysis in a single test, covering key genes implicated in various disease pathways.

  2. High Sensitivity and Specificity: Utilizing Illumina’s proven next-generation sequencing (NGS) technology, the TrueSight One Panel delivers high sensitivity and specificity for detecting genetic variants, including single nucleotide variants (SNVs), insertions, deletions, and copy number variations (CNVs). Its high analytical sensitivity enables the detection of rare and low-frequency variants, ensuring accurate and reliable results.

  3. Customizable Content: The TrueSight One Panel offers customizable content, allowing laboratories to tailor the panel to specific clinical indications or patient populations. This customization capability enables laboratories to add or remove genes of interest, incorporate updated gene content, or target specific regions within genes for deeper coverage, enhancing flexibility and relevance in clinical testing.

  4. Streamlined Workflow: Featuring a streamlined workflow, from sample preparation to data analysis, the TrueSight One Panel facilitates efficient and cost-effective genetic testing in clinical laboratories. The panel includes standardized protocols and bioinformatics pipelines for sample processing, sequencing, variant calling, and interpretation, reducing complexity and accelerating turnaround times.

  5. Clinical Validation: The TrueSight One Panel has undergone rigorous clinical validation to ensure its accuracy, reliability, and clinical utility for genetic testing in clinical practice. It has been extensively validated across diverse patient populations and sample types to demonstrate its performance in detecting clinically relevant genetic variants associated with inherited diseases.

  6. Regulatory Compliance: Designed to meet regulatory requirements for clinical diagnostic testing, including compliance with quality assurance standards and guidelines issued by regulatory agencies such as the U.S. Food and Drug Administration (FDA) and the Centers for Medicare & Medicaid Services (CMS), the TrueSight One Panel meets the highest standards for clinical laboratory testing and patient care.

How Can the Illumina TrueSight One Panel be used?

The Illumina TrueSight One Panel can be used in clinical settings for various applications related to genetic analysis and molecular diagnostics. Here are some ways in which the TrueSight One Panel can be utilized:

  1. Clinical Diagnosis: The TrueSight One Panel can be used for the diagnosis of inherited diseases and genetic disorders. By sequencing clinically relevant genes associated with various conditions, the panel can help identify pathogenic variants responsible for a patient’s symptoms or clinical presentation. This information can assist clinicians in confirming a diagnosis, predicting disease progression, and informing treatment decisions.

  2. Risk Assessment: The TrueSight One Panel can aid in assessing an individual’s genetic predisposition to certain diseases and conditions. By identifying disease-associated variants, the panel can provide insights into a patient’s risk of developing specific disorders, such as cancer predisposition syndromes or cardiovascular diseases. This information can inform preventive measures, screening recommendations, and lifestyle modifications to reduce disease risk.

  3. Pharmacogenomic Testing: The TrueSight One Panel includes genes associated with drug metabolism and response, making it suitable for pharmacogenomic testing. By analyzing genetic variants known to influence drug efficacy, toxicity, and metabolism, the panel can help guide personalized medication selection, dosing optimization, and medication management strategies. This can improve medication safety and efficacy while minimizing the risk of adverse drug reactions.

  4. Carrier Screening: The TrueSight One Panel can be used for carrier screening to assess an individual’s risk of passing on genetic disorders to their offspring. By identifying carrier status for recessive genetic conditions, the panel can provide valuable information to individuals or couples planning a family. This information can inform reproductive decision-making, including family planning and prenatal testing options.

  5. Cancer Profiling: The TrueSight One Panel can be applied in oncology for cancer profiling and molecular characterization of tumors. By analyzing cancer-related genes, the panel can identify somatic mutations, copy number alterations, and other genomic alterations associated with tumor development and progression. This information can help guide cancer diagnosis, prognosis, treatment selection, and monitoring of treatment response.

  6. Research Studies: The TrueSight One Panel can be used in research studies and clinical trials to investigate the genetic basis of diseases, identify novel disease-associated variants, and explore genotype-phenotype correlations. By leveraging its comprehensive gene coverage and high-throughput sequencing capabilities, the panel can support genomics research across various fields, including rare diseases, population genetics, and precision medicine.

How does this panel help with studying health issues?

The Illumina TrueSight One Panel plays a significant role in studying health issues by providing valuable genetic information that can inform research on various aspects of human health and disease. Here’s how the panel helps in studying health issues:

  1. Identification of Disease-Causing Variants: The TrueSight One Panel enables the identification of genetic variants associated with inherited diseases and disorders. By sequencing clinically relevant genes implicated in various health conditions, the panel helps researchers pinpoint pathogenic variants responsible for disease development. This information is crucial for understanding the genetic basis of diseases and elucidating their underlying mechanisms.

  2. Genotype-Phenotype Correlation Studies: The TrueSight One Panel facilitates genotype-phenotype correlation studies by correlating genetic variants with clinical phenotypes and disease outcomes. Researchers can analyze the relationship between specific genetic mutations and disease manifestations, severity, progression, and treatment response. This information enhances our understanding of disease heterogeneity, prognosis, and personalized medicine approaches.

  3. Population Genetics and Epidemiology: The TrueSight One Panel supports population genetics and epidemiological studies by analyzing genetic variation across diverse populations and ethnic groups. Researchers can investigate the prevalence, distribution, and frequency of disease-associated variants in different populations, shedding light on population-specific genetic risk factors and ancestry-related health disparities.

  4. Rare Disease Research: The TrueSight One Panel aids in rare disease research by identifying rare and novel genetic variants associated with rare and undiagnosed conditions. By sequencing genes implicated in rare genetic disorders, the panel helps researchers uncover rare pathogenic variants, expand the genotype-phenotype spectrum of rare diseases, and facilitate diagnosis and treatment for affected individuals.

  5. Pharmacogenomics Research: The TrueSight One Panel supports pharmacogenomics research by analyzing genetic variants involved in drug metabolism and response. Researchers can investigate the impact of genetic variation on drug efficacy, toxicity, and pharmacokinetics, informing precision medicine approaches and personalized drug therapies. This information contributes to the development of pharmacogenomic guidelines and optimization of drug treatment strategies.

  6. Cancer Genomics Studies: The TrueSight One Panel is valuable for cancer genomics research by characterizing genetic alterations in cancerous tumors. Researchers can analyze somatic mutations, copy number alterations, and other genomic changes associated with cancer development, progression, metastasis, and treatment resistance. This information aids in the discovery of cancer biomarkers, development of targeted therapies, and advancement of precision oncology.

Overall, the Illumina TrueSight One Panel serves as a powerful tool for studying health issues across diverse research areas, including genetics, genomics, epidemiology, pharmacology, and oncology. Its comprehensive gene coverage, high sensitivity and specificity, customizable content, and clinical validation make it an indispensable resource for advancing our understanding of human health and disease.

Can the Illumina TrueSight One Panel work with computers?

Yes, the Illumina TrueSight One Panel can be used in conjunction with computers for data analysis, interpretation, and reporting of genetic sequencing results. Here’s how the TrueSight One Panel works with computers:

  1. Data Analysis: After sequencing DNA samples using the TrueSight One Panel, the raw sequencing data generated by the Illumina sequencing platform is transferred to a computer for data analysis. Bioinformatics software and pipelines are used to process the raw sequencing reads, align them to a reference genome or transcriptome, identify genetic variants (e.g., single nucleotide polymorphisms, insertions, deletions), and annotate their functional consequences.

  2. Variant Calling: Bioinformatics algorithms are employed to call genetic variants from the aligned sequencing data. These algorithms compare the sequence reads from the patient’s sample to a reference genome, identifying differences (variants) such as single nucleotide changes, small insertions or deletions, and larger structural variations. Variant calling software runs on computers to perform this task efficiently.

  3. Variant Annotation and Interpretation: Once genetic variants are identified, bioinformatics tools are used to annotate their functional consequences and assess their potential clinical significance. Variant annotation involves assigning functional annotations (e.g., location within a gene, predicted impact on protein structure or function) and population frequency data to each variant. Variant interpretation involves determining the clinical relevance of variants based on existing knowledge of genotype-phenotype associations, disease databases, and professional guidelines.

  4. Data Visualization and Reporting: Bioinformatics software allows researchers and clinicians to visualize sequencing data and genetic variants in graphical formats. This includes generating variant allele frequency plots, sequence alignments, and gene diagrams. Additionally, software tools facilitate the generation of comprehensive variant reports that summarize the identified variants, their clinical significance, and recommendations for patient management.

  5. Storage and Management: Computers are used to store, manage, and analyze large volumes of sequencing data generated by the TrueSight One Panel. This includes maintaining secure databases and storage systems for storing sequencing data, metadata, and analysis results. Advanced computing infrastructure, including high-performance computing clusters and cloud-based platforms, may be utilized to handle the computational demands of NGS data analysis.

Overall, computers play a critical role in the analysis and interpretation of sequencing data generated by the Illumina TrueSight One Panel, enabling researchers and clinicians to extract meaningful insights from genetic data and apply them to clinical practice and research.